Package: Category

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.18.0.tar.gz

StartedAt: 2011-10-20 14:00:39 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:04:58 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 258.2 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Category.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.18.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Category' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'Category.pdf' from 813Kb to 293Kb
     compacted 'ChromBand.pdf' from 560Kb to 249Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'Category' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Category)

name	user	system	elapsed
ChrBandTree-class	21.517	0.629	26.216
ChrMapHyperGParams-class	0.002	0.000	0.002
ChrMapHyperGResult-class	0.001	0.000	0.001
ChrMapLinearMParams-class	0.001	0.001	0.001
ChrMapLinearMResult-class	0.001	0.000	0.002
DatPkg-class	0.112	0.008	0.167
HyperGResult-accessors	1.349	0.101	1.625
LinearMParams-class	0.001	0.000	0.001
LinearMResult-class	0.001	0.000	0.001
LinearMResultBase-class	0.001	0.001	0.002
MAPAmat	16.921	0.706	22.335
applyByCategory	0.004	0.001	0.004
cateGOryMatrix	0.487	0.085	0.611
cb_parse_band_Hs	0	0	0
cb_parse_band_Mm	0.001	0.001	0.001
findAMstats	0.002	0.000	0.002
getPathNames	0.215	0.017	0.432
gseattperm	6.693	0.200	8.546
makeChrBandGraph	14.988	0.268	19.404
makeEBcontr	0.757	0.017	0.937
probes2MAP	0.378	0.017	0.494
probes2Path	0.120	0.007	0.130
ttperm	0.044	0.003	0.047